Containment of a multi-index B.1.1.7 outbreak on a university campus through a genomically-informed public health response

  1. Emily T. Martin
  2. Adam S. Lauring
  3. JoLynn P. Montgomery
  4. Andrew L. Valesano
  5. Marisa C. Eisenberg
  6. Danielle Sheen
  7. Jennifer Nord
  8. Robert D. Ernst
  9. Lindsey Y. Mortenson
  10. Riccardo Valdez
  11. Yashar Niknafs
  12. Darryl Conway
  13. Sami F. Rifat
  14. Natasha Bagdasarian
  15. Sarah Lyon-Callo
  16. Jim Collins
  17. Heather Blankenship
  18. Marty Soehnlen
  19. Juan Marquez

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Abstract

The first cluster of SARS-CoV-2 cases with lineage B.1.1.7 in the state of Michigan was identified through intensive university-led surveillance sampling and targeted sequencing. A collaborative investigation and response was conducted by the local and state health departments, and the campus and athletic medicine COVID-19 response teams, using S-gene target failure screening and rapid genomic sequencing to inform containment strategies. A total of 50 cases of B.1.1.7-lineage SARS-CoV-2 were identified in this outbreak, which was due to three coincident introductions of B.1.1.7-lineage SARS-CoV-2, all of which were genetically distinct from lineages which later circulated in the broader community. This investigation demonstrates the successful implementation of a genomically-informed outbreak response which can be extended to university campuses and other settings at high risk for rapid emergence of new variants.

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  1. ScreenIT

    SciScore for 10.1101/2022.01.04.22268758: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    EthicsIRB: Human Subjects Approval: Sequencing of samples was approved by the University of Michigan Institutional Review Board (IRB Protocol ID: HUM185966) or performed as part of a public health investigation prompted by state and local health officials (IRB Protocol ID:
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Phylogenetic methods: To generate a phylogenetic tree, we aligned consensus genomes with MUSCLE 3.8.31 and masked positions that are known to commonly exhibit homoplasies or sequencing errors(8).
    MUSCLE
    suggested: (MUSCLE, RRID:SCR_011812)
    We generated a maximum likelihood phylogeny with IQ-TREE, using a GTR model and 1000 ultrafast bootstrap replicates(9,10).
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    For saliva specimens, RNA was extracted with the Thermo Fisher MagMAX Viral RNA Isolation Kit (200 µL of input sample eluted in 50 µL).
    Thermo Fisher MagMAX
    suggested: None
    Reads were aligned to the Wuhan-Hu-1 reference genome (GenBank MN908947.3) with BWA-MEM version 0.7.15.
    BWA-MEM
    suggested: (Sniffles, RRID:SCR_017619)
    Oxford Nanopore library preparation and sequencing: After multiplex PCR amplification, libraries were prepared for sequencing with the Oxford Nanopore Technologies MinION using the ARTIC Network version 3 protocol (6,7).
    Oxford Nanopore
    suggested: (Oxford Nanopore Technologies, RRID:SCR_003756)
    Each library (15-20 ng) was loaded onto a flow cell (FLO-MIN106) and sequenced with the MinION.
    MinION
    suggested: (MinION, RRID:SCR_017985)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2022.01.04.22268758v1 on medRxiv